GEO DataSets

(Submitter supplied) Agilent 25 mers

Organism:

Eucalyptus

3 Series

64 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Eucalyptus grandis x Eucalyptus urophylla; Eucalyptus

Type:

Expression profiling by array; Other

Platforms:

GPL10916 GPL10939

192 Samples

Download data: TXT

(Submitter supplied) Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. more...

Organism:

Eucalyptus grandis x Eucalyptus urophylla; Eucalyptus

Type:

Expression profiling by array; Other

Platforms:

GPL10916 GPL10939

136 Samples

Download data: TXT

(Submitter supplied) Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. more...

Organism:

Eucalyptus grandis x Eucalyptus urophylla; Eucalyptus

Type:

Expression profiling by array; Other

Platform:

GPL10916

56 Samples

Download data: TXT

(Submitter supplied) Agilent 25 mers

Organism:

Eucalyptus

2 Series

128 Samples

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(Submitter supplied) The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars.

Organism:

Oryza sativa; Oryza sativa Indica Group; Oryza sativa Japonica Group

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL2025

27 Samples

Download data: CEL, CHP

(Submitter supplied) Genotyping arrays are tools for high throughput genotyping, which is required in genome-wide association studies (GWAS). Since the first cucumber genome draft was reported, genetic maps were constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and other sequence-related amplified polymorphism (SRAP). In this study we developed the first cucumber genotyping array which consisted of 32,864 single nucleotide polymorphisms (SNPs). more...

Organism:

Cucumis sativus

Type:

Genome variation profiling by SNP array

Platform:

GPL18647

150 Samples

Download data: TXT

(Submitter supplied) The gene expression profiles of the differentiating xylem of 91 Eucalyptus grandis backcross individuals were characterized following a loop design (Churchill, G.A. Nat Genet. 2002 Dec;32 Suppl:490-5). In this design, RNA from genotype 1666 (labeled with Cy5) was hybridized with RNA from genotype 1667 (labeled with Cy3) on the first slide(GEO accession number GSM7637); the same genotype 1667 (now labeled with Cy5) was compared with genotype 1669 (Cy3) on the second slide (GSM7638), and so on. more...

Organism:

Eucalyptus grandis; Eucalyptus tereticornis

Type:

Expression profiling by array

Platform:

GPL348

91 Samples

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(Submitter supplied) Comparison of mRNA accumulation in segregating doubled haploid barley lines ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, . The equivalent experiment is BB21 at PLEXdb.]

Organism:

Hordeum vulgare

Type:

Expression profiling by array

Platform:

GPL1340

41 Samples

Download data: CEL

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...

Organism:

Eucalyptus grandis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20030

5 Samples

Download data: BEDGRAPH

(Submitter supplied) Background: Cowpea (Vigna unguiculata L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP) is a microarray-based marker which can be used for high throughput genotyping and high density mapping. more...

Organism:

Glycine max; Vigna unguiculata

Type:

Expression profiling by array

Platform:

GPL4592

8 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions. Results: Gene specific linear mixed models were fit to each of the log2 transformed probe intensities on these arrays, using fixed effects for breed, probe, breed-by-probe interaction, and a random effect for array. more...

Organism:

Sus scrofa

Type:

Expression profiling by genome tiling array

Platform:

GPL6472

6 Samples

Download data: CEL

(Submitter supplied) Background: Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions. This dataset uses different tissue types to explore the consequences of additional sample variance. more...

Organism:

Sus scrofa

Type:

Expression profiling by genome tiling array

Platform:

GPL6472

6 Samples

Download data: CEL

(Submitter supplied) See manufacturer's website.

Organism:

Zea mays

1 Series

2290 Samples

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(Submitter supplied) Advances in alfalfa [Medicago sativa (L.) subsp. sativa] breeding, molecular genetics and genomics have been slow because this crop is an allogamous autotetraploid (2n = 4x = 32) with complex polysomic inheritance. Increasing cellulose and decreasing lignin in alfalfa stem cell walls would improve this crop as a cellulosic ethanol feedstock. We selected two alfalfa genotypes (252, 1283) that differ in cellulose and Klason lignin concentration in stem cell walls. more...

Organism:

Medicago sativa; Medicago truncatula; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL4652

12 Samples

Download data: CEL

(Submitter supplied) In order to pinpoint the most differentially expressed genes between Eucalyptus grandis leaf blades and vascular (xylem) tissues as well as between E. grandis and Eucalyptus globulus xylem tissues, a total number of nine 50mer-oligoprobes covering the length of each one of 21,432 unique sequences derived from the Genolyptus EST dataset were synthesized “on-chip” in duplicate, randomly distributed in two blocks of each slide. more...

Organism:

Eucalyptus globulus; Eucalyptus grandis; Eucalyptus spp. mixed library

Type:

Expression profiling by array

Platform:

GPL14357

10 Samples

Download data: FTR, TXT

(Submitter supplied) Background: Eucalyptus species and interspecific hybrids exhibit valuable growth and wood properties that make them a highly desirable commodity. However, these trees are challenged by a wide array of biotic stresses during their lifetimes. The Eucalyptus grandis reference genome sequence provides a resource to study pest and pathogen defence mechanisms in long-lived woody plants. E. grandis trees are generally susceptible to Chrysoporthe austroafricana, a causal agent of stem cankers on eucalypts. more...

Organism:

Eucalyptus grandis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19989

12 Samples

Download data: TXT

(Submitter supplied) Purpose: Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. more...

Organism:

Eucalyptus nitens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18542

12 Samples

Download data: TXT

(Submitter supplied) Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate. After 10 days, half the plants were harvested (total root tissue). At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions. Root tissue was harvested for the remaining plants at 14 days after planting. more...

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL4592

24 Samples

Download data: CEL

(Submitter supplied) Purpose: Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection Methods: We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. more...

Organism:

Eucalyptus camaldulensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15809

12 Samples

Download data: TXT